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AllenInstitute / abc_atlas_access

Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
https://alleninstitute.github.io/abc_atlas_access/
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Questions about registering spatial transcriptome data with CCF #42

Open Super-LzzZ opened 9 months ago

Super-LzzZ commented 9 months ago

Hi !!!

what a great jobs !!!

I have some questions about registering spatial transcriptome data with CCF:

1) In the "merfish_ccf_registration_tutorial.ipynb" demo, I noticed that the data "MERFISH-C57BL6J-638850-CCF" has the corresponding "image_volumes", the matching image information can be determined through the z-axis. Does the image information come from CCF or is it generated in the experiment?

2) In the ‘zhuang_merfish_tutorial.ipynb’ demo, I observed that this data does not have ‘image_volumes,’ but it still provides CCF coordinates after registration. Is there any information available to specify which CCF slice each individual section is registered to?"

Thank !!!

morriscb commented 8 months ago

Hi @Super-LzzZ,

If you have scientific questions or questions about the data itself, your best place to find answers will be on the Allen Institute community forum: https://community.brain-map.org/ I'm sure someone can answer your questions there.

The issues to post here will be if you are running into problems with the code in this repo or are finding bugs in the notebooks/website.

Good luck! Chris